SMTL ID : 8ea9.1

NKG2D complexed with inhibitor 4d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-dimer

Ligands

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 6 residues within 4Å: Chain A: Y.65, I.95, A.106, S.107, K.110, Y.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.107, A:K.110, A:Y.112

1 x VMQ: N-[(1S)-1-[3,5-bis(trifluoromethyl)phenyl]-2-(dimethylamino)-2-oxoethyl]-4-[4-(trifluoromethyl)phenyl]pyridine-3-carboxamide(Non-covalent)

VMQ.2: 16 residues within 4Å: Chain A: I.17, F.26, L.58, L.61, V.62, K.63, H.66 Chain B: I.17, Y.24, Q.25, F.26, L.58, L.61, V.62, K.63, I.123 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:L.61, A:K.63, B:K.63 Hydrophobic interactions: B:I.17, B:F.26, B:F.26, B:L.61, B:I.123 pi-Stacking: B:F.26

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 7 residues within 4Å: Chain A: N.15, Q.25, F.26 Chain B: Y.19, D.57, L.58, L.61 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.19, A:F.26 PEG.4: 9 residues within 4Å: Chain A: Y.19, D.57, L.58, L.61 Chain B: N.15, I.17, Y.24, Q.25, F.26 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:F.26 Water bridges: A:D.57, A:K.60

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 7 residues within 4Å: Chain B: N.44, S.46, K.49, Y.51, M.125, Q.126, R.127 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thompson, A.A. et al., Identification of small-molecule protein-protein interaction inhibitors for NKG2D. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-05-03

Peptides

NKG2-D type II integral membrane protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

NKG2-D type II integral membrane protein

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